Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1460 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0105481517 sf0105480517 1 5481517 1.37E-07 1.01E-06
vg0804956339 sf0804955342 8 4956339 2.26E-07 1.01E-07
vg0405830585 sf0405826024 4 5830585 1.18E-06 3.49E-06
vg0624108904 sf0624107907 6 24108904 1.33E-06 2.63E-07
vg0105385456 sf0105384456 1 5385456 8.57E-06 1.01E-08
vg0220169813 sf0220163945 2 20169813 NA 3.63E-06
vg0211308829 sf0211308826 2 11308829 NA 4.17E-06
vg0105475832 sf0105474832 1 5475832 NA 4.78E-06